Proteins may be thought of as string with beads on it. Each bead has a particular color. For many proteins, there are 20 colors, or 20 different beads. The string folds up in a certain way, which means that it ends up with a certain series of folds. When profiling a protein, researchers attempt to determine the order of the colors of the beads and where the beads are in three-dimensional space. These locations are important because all of the bodily functions depend on this three-dimensional structure. An important problem is determining how hundreds of thousands of proteins fold.
Many proteins are globular and form in an intracellular environment or plasma, which are both aqueous environments. For these proteins, it can be assumed that there are only two colors, blue and red. Blue beads (called “hydrophobic”) do not like water and red beads (called “hydrophilic”) are attracted to water. When these types of globular proteins fold up, all of the blue beads get in the center and the red beads are on the outside of the protein. Consequently, the residues that like water are on the outside and the residues that do not like water are on the inside. A protein formed in this manner will have a hydrophobic core and a hydrophilic exterior.
The structure of globular proteins can actually be quite complex, and contain substructures such as beta sheets, beta strands, alpha-helices, and other helices. Because the structure of the protein affects the way that the protein interacts with its environment (and vice versa), protein structures have been studied in detail. A computational technique for studying proteins includes mathematically modeling protein structure to determine primary, secondary, tertiary, and even quaternary protein structures.
Many of these techniques examine details associated with proteins, such as determining exactly where residues are or the exact order of residues. Few of these techniques are suitable for analyzing an entire protein. Even fewer of the these techniques can accurately determine whether a man-made protein structure is or could be a real protein.
Thus, what is needed is a better way of quantifying and analyzing protein structure and a better way to determine if an example protein structure is or could be a real protein.